LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp 275.0 275.0 100.0 tchain 1

shell "rm -f peptide2.colvars.*"
fix		2 all colvars peptide.colvars2 output peptide2

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles

#dump		1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars:  https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars2":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "one"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new "harmonic" instance.
colvars:   # name = "h_pot"
colvars:   # colvars = { one }
colvars:   # outputEnergy = off [default]
colvars:   # timeStepFactor = 1 [default]
colvars:   # writeTISamples = off [default]
colvars:   # writeTIPMF = off [default]
colvars:   # centers = { 10 }
colvars:   # targetCenters = { 10 } [default]
colvars:   # outputCenters = off [default]
colvars:   # forceConstant = 100
colvars:   # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "peptide2.colvars.state".
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
SHAKE stats (type/ave/delta) on step 100
  4 1.11096 0.000191462
  6 0.996989 3.55508e-05
  8 1.08 9.0997e-06
  10 1.111 1.58544e-05
  12 1.08 5.80604e-06
  14 0.959997 0
  18 0.957198 2.92445e-05
  31 104.52 0.00239923
     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
colvars: Saving collective variables state to "peptide2.colvars.state".
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms

Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.6373     | 1.6373     | 1.6373     |   0.0 | 72.46
Bond    | 0.0031531  | 0.0031531  | 0.0031531  |   0.0 |  0.14
Kspace  | 0.17439    | 0.17439    | 0.17439    |   0.0 |  7.72
Neigh   | 0.40442    | 0.40442    | 0.40442    |   0.0 | 17.90
Comm    | 0.014091   | 0.014091   | 0.014091   |   0.0 |  0.62
Output  | 0.00027752 | 0.00027752 | 0.00027752 |   0.0 |  0.01
Modify  | 0.024481   | 0.024481   | 0.024481   |   0.0 |  1.08
Other   |            | 0.001465   |            |       |  0.06

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11143 ave 11143 max 11143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708234 ave 708234 max 708234 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
colvars: Resetting the Collective Variables module.

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:02
